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# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack.package import *
class RRsamtools(RPackage):
"""Binary alignment (BAM), FASTA, variant call (BCF), and tabix file
import.
This package provides an interface to the 'samtools', 'bcftools', and
'tabix' utilities for manipulating SAM (Sequence Alignment / Map),
FASTA, binary variant call (BCF) and compressed indexed tab-delimited
(tabix) files."""
bioc = "Rsamtools"
version('2.12.0', commit='d6a65dd57c5a17e4c441a27492e92072f69b175e')
version('2.10.0', commit='b19738e85a467f9032fc7903be3ba10e655e7061')
version('2.6.0', commit='f2aea061517c5a55e314c039251ece9831c7fad2')
version('2.2.1', commit='f10084658b4c9744961fcacd79c0ae9a7a40cd30')
version('2.0.3', commit='17d254cc026574d20db67474260944bf60befd70')
version('1.34.1', commit='0ec1d45c7a14b51d019c3e20c4aa87c6bd2b0d0c')
version('1.32.3', commit='0aa3f134143b045aa423894de81912becf64e4c2')
version('1.30.0', commit='61b365fe3762e796b3808cec7238944b7f68d7a6')
version('1.28.0', commit='dfa5b6abef68175586f21add7927174786412472')
depends_on('r@3.5.0:', type=('build', 'run'), when='@2.10.0:')
depends_on('r-genomeinfodb@1.1.3:', type=('build', 'run'))
depends_on('r-genomicranges@1.21.6:', type=('build', 'run'))
depends_on('r-genomicranges@1.31.8:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-biostrings@2.37.1:', type=('build', 'run'))
depends_on('r-biostrings@2.47.6:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-biocgenerics@0.1.3:', type=('build', 'run'))
depends_on('r-biocgenerics@0.25.1:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-s4vectors@0.13.8:', type=('build', 'run'))
depends_on('r-s4vectors@0.17.25:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-iranges@2.3.7:', type=('build', 'run'))
depends_on('r-iranges@2.13.12:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-xvector@0.15.1:', type=('build', 'run'))
depends_on('r-xvector@0.19.7:', type=('build', 'run'), when='@1.32.3:')
depends_on('r-zlibbioc', type=('build', 'run'))
depends_on('r-bitops', type=('build', 'run'))
depends_on('r-biocparallel', type=('build', 'run'))
depends_on('r-rhtslib@1.16.3', type=('build', 'run'), when='@2.0.3')
depends_on('r-rhtslib@1.17.7:', type=('build', 'run'), when='@2.2.1:')
depends_on('gmake', type='build')
# this is not a listed dependency but is needed
depends_on('curl')
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